Once the basis was used up, were the losses being carried over every year?   What happens with that amount this year?   

All of the losses have been suspended, but can be recognized this year due to the disposal.  

Is this just an arithmetic problem?  Cash out minus cash in should equal gains on Schedule D minus losses on Schedule E.  If not, at least you have a clue about where to look for explanation.  

Whenever I saw a sale of a PTP on both the K-1 and 1099, I entered both but also made an entry to zero out the 1099 entry SINCE IT WAS WRONG AS YOU STATED. The 1099 basis was the original cost.

The K-1 sale entry would correctly report any gain or loss and any recapture.

I wish it were that straight forward.  There are Section 751 adjustments as well as 163(j) adjustments.  The basis has been adjusted downward over the life of the investment.  

Somewhere on the 20 pages of PTP K-1 and inductions they tell you how and where to report the sale, and give you most of the numbers (or how to compute them)

Remember that basis in a partnership is not what you originally invested.

I have seen 1099s from full-service brokers where the cost basis matches what is shown on the K-1. Your results may differ; that’s why it’s important to match cash out minus cash in, with the income shown on the return. And attach a computation of how you reached that result. You’re talking about real money here, not just numbers on a page.

I am using the Schedule of Sales in the K-1.  The only item I am still have an issue with is the 163(j) deduction.  The software does not handle it and so I entered it manually on schedule E.  This is creating an error on "Error Check" because I had to manually override a field.  Any thoughts on how to enter this differently?

My point exactly. See sjrcpa's response.